The Awful Chemical Language

I was often asked to explain chemical nomenclature in the context of such and such intellectual property law matter and one day I surprised a trial lawyer — an elderly gent — with my knowledge. He was actually annoyed at first, perhaps because he felt hostage to knowledge which he did not possess. Actually, he probably just resented that I could bill time for knowledge which I already possessed — just like he could. Had he known what it had cost me to acquire my art, he would also have known that it would break any law firm to buy it. Meanwhile, I had been hard at work learning legal terminology for several weeks, and although I had made good progress, it had been accomplished under great difficulty and annoyance. But he was greatly impressed and after I had explained a while, he said my explanation of the chemical language was very rare, possibly "unique" and he wanted to add me to his litigation team.

Friedrich Wöhler, the father of modern organic chemistry, already remarked in 1835:

Organic chemistry just now is enough to drive one mad. It gives me the impression of a primeval forest full of the most remarkable things, a monstrous and boundless thicket, with no way of escape, into which one may well dread to enter.

A person who has not studied chemistry — especially organic chemistry — can form no idea of what a perplexing language describes that thicket. Or perhaps they can, but can come up with no logical explanation for why things are so. I aim here to simplify.

The Germans invented modern organic chemistry and they logically fashioned the nomenclature in their own image — and just as the German language is troublesome for the beginner — having so many parts of speech — it's no wonder organic nomenclature is so troublesome.

An average organic chemical name is a sublime and impressive curiosity; it may occupy several lines and comprise several unfamiliar names and numbers — things called moieties — and even Greek letters; it is built mainly of compound words synthesized by the writer around a core or parent name; it's quite often a word not to be found in any normal dictionary — several words compacted into one, but with joints and seams — that is, with hyphens; it may treat of up to umpteen different subunits, each enclosed in a parenthesis of its own, with here and there extra parentheses which reinclose three or four of the minor parentheses, making pens within pens: finally, all the parentheses and re-parentheses are massed together between a couple of king-parentheses, one of which is placed in the first line of the majestic structure and the other in the middle of the last line of it — after which comes the parent compound name, and you find out for the first time what the molecule is or at least what some chemical lexicographer thought it should be derived from. Sometimes, often as an afterthought — merely by way of differentiation — the writer shovels in the name of a salt, or in patent parlance "or salts thereof," signifying that the delicate molecular flower has been preserved as a salt, and the monument is finished. I suppose that this closing hurrah is often the doing of patent attorneys seeking to claim more broadly; it's not necessary, but covers the doctrine of equivalents.

To repeat, organic chemistry nomenclature was invented by 19th century Germans who wanted to create a simple system which closely mimicked the logic of their own language. Full stop. Therein lies the secret why that nomenclature is so seemingly obtuse — it is patterned after German syntax. In linguistics, syntax refers to the way in which morphemes are arranged. By analogy, "chemical morphemes" are irreducible units of metaphor — core words like "meth-," eth-," "prop-," and "but-" and ringed ones like "phen-" or "benz-" represent chemical entities. [1]  The studied reader may already recognize these morphemes in methane, ethane, propane, butane, phenyl, and benzene and the like. The endings "ane," "yl," and "ene" are, in a linguistic sense, inflections of the morphemes. Another word related to morphemes commonly used by chemists is moiety. Moiety refers to small clusters of recognizable function, for example, "acyl," carboxyl," "alkyl," etc.

By way of example, consider the common pain reliever ibuprofen which more properly goes by the name
RS-2-(4-(2-methylpropyl)phenyl)propanoic acid.

Chemical names are easier to read when you hold them next to the actual structure which is like a pictograph (hold that thought for later) or read them backwards in a mirror or stand on your head — so as to reverse the construction -- but because many refuse to learn the real language of chemistry — structural short hand — I'll muddle through the name of ibuprofen by way of example.  It's not a particularly elaborate molecule or name, but it strikes a nice balance between complexity and simplicity.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

First comes "R,S." The "R" stands for rectus (Latin for right) and the "S" stands for sinister (Latin for left). This gives the enlightened reader notice that chirality is at hand — more on this later.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

The second element in the name is the number 2, and because this number stands alone — outside of parentheses — the reader is asked to hold its meaning in abeyance until such a time as the parent morpheme is finally reached after much exhaustion of patience. Putting the "2" in front resembles the dreaded separable prefix verbs so common to German. Mark Twain wrote in his delightful essay, The Awful German Language:

The Germans have another kind of parenthesis, which they make by splitting a verb in two and putting half of it at the beginning of an exciting chapter and the other half at the end of it. Can any one conceive of anything more confusing than that? These things are called "separable verbs." The German grammar is blistered all over with separable verbs; and the wider the two portions of one of them are spread apart, the better the author of the crime is pleased with his performance.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

The third element, (4-(2-methylpropyl)phenyl) is a microcosm of the whole name writ larger; in it we have a 2-methylpropyl corralled by parentheses, which is itself corralled by "4-" and "phenyl." The name is starting to look like a matryoshka doll.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

At long last we arrive at the parent morpheme, which like the verb in a German sentence, tells us the key information: propanoic acid. In the lexicographer's mind, ibuprofen is a derivative of propanoic acid.

We have the germanic parenthesis disease in our language, too; also often expressed with em dashes and sometimes elipses and one may see cases of it every day in our books and blog posts: but with us it is — unless botched — the mark and sign of a practiced writer or a clear intellect, whereas with the Germans and chemical lexicographers it is doubtless the mark and sign of a practiced pen and of the presence of that sort of luminous intellectual fog which stands for clearness among these people. For surely it is not clearness — it necessarily can't be clearness.

Now dear reader, allow me to introduce a better way to depict all the foregoing and to illustrate the  foolishness:

Ibuprofen

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

I have color-coded the three main parts of the molecule, both in name and in the depiction. The reader immediately grasps that the red propanoic acid portion has a three carbon chain. The red number "2" in the name describes wherefrom the rest depends. The "R,S" refers to the two possible ways that the invisible hydrogen atom attached to carbon 2 may point: either out of or into to the screen or page. The portion circled in light blue is a phenyl moiety having six carbons numbered as shown. The curious reader can attest that the portion in green indeed appends from carbon 4 of the blue phenyl. The left-most portion — circled in green — is the "2-methylpropyl" portion: it's really a 3-carbon propyl chain having a methyl affixed to carbon 2.

Lastly, it is perhaps now apparent (to me at least) where the trivial name ibuprofen comes from: I parse ibuprofen into three separable pieces: ibu/pro/fen

"ibu" is short for "isobutyl (another name for 2-methylpropyl;"
"pro" is short for "propanoic acid;"
"fen" stands for "phenyl."

Have you got a headache yet?
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Suggested further reading:

[1] An Algorithm For Translating Chemical Names To Molecular Formulas
[2] Development Of Systematic Names For The Simple Alkanes

Vanadium Adds Color

Vanadium is the first element of color. The previous element, titanium, is actually the essence of butt-white: Titanium dioxide, TiO₂ is commonly used in white paint and also as a sunscreen. Of all the other previous elements, only chlorine is a pretty lime green. I suppose that sulfur counts as yellow and boron counts as brown, and certain allotropes of carbon counts as black--but only as solids. By "element of color" I mean that vanadium is the first of many elements that form pretty colored water solutions:
 

Oxidation states of vanadium, from left +2 (lilac), +3 (green), +4 (blue) and +5 (yellow).

There's a reason why vanadium does this, but I'm going to hold off a simplified explanation until I get to chromium (nominally the best example).

Vanadium's discovery is a bit sad in that its true discoverer, a fellow named del Rio, was talked out of his discovery by a Frenchman. Our old friend Friedrich Wöhler showed up and straightened things out, but not before the Swedish name stuck. The whole naming history is here.

Vanadium has an oxidation state of +5 in the oxide VO₅.  VO₅ has nothing to do with the shampoo VO5, but I thought that the first photo bore such a striking likeness to the second one that I put it here just to confuse things.

In the Periodic Table, vanadium belongs to Group 5. Chemistry students recognize the convenient mnemonic for vanadium (V is five in Roman numerals). 

Most of the world's mined vanadium goes into steel where it alloyed with iron to improve its strength. Vanadium also has some very interesting biological properties and may even be a micro nutrient essential to humans (it is essential to rats and chickens). It also appears to have promise in high-tech batteries.

Aluminum

Van der Krogt's piece on aluminum is so fascinating, and so thorough regarding the discovery and naming of the 13th element that I suggest people go there for those aspects. Coincidentally, Friedrich Wöhler was involved in aluminum's discovery.

Aluminum, once considered a precious metal, is the third most abundant element on earth, after silicon and oxygen. Aluminum was so dear at one time that the Washington Monument was capped with pyramidal shaped cast of it. link  It's still up there. Aluminum was only precious because it was so hard to make in quantity in a pure form. The invention of the electric dynamo by Siemens dropped the price a thousand-fold.

Aluminum reacts spontaneously with oxygen and yet, never completely. Aluminum exemplifies a metallic property called passivation. Passivation occurs when a metal coats itself with a thin layer of its own oxide, thus protecting its inner mass from attack. It's a bit like sacrificing your skin to your enemy in self defence. This property only works if the oxide layer has the same physical density as the underlying inner metal. Anodized aluminum is a related technique of passivation and decorative colors may be introduced. Iron rusts so easily because the initially formed layer of rust shrinks and cracks the surface, exposing more fresh metal underneath and so on and so forth.

Political passivation entails coating oneself with a thin skin of your enemy's element.

Taking the Piss out of Vitalism



Friedrich Wöhler (1800-1882)

The notion that matter from living beings essentially differs from matter derived from non-living sources used to be called vitalism. Vestiges still remain. Historically, the terms "organic" and "inorganic" delineated the chemistry of life from the chemistry of inanimate matter. Over time, "organic chemistry" morphed into the generic chemistry of carbon and, within that genus, biochemistry came to mean the chemistry of living things. This left "inorganic chemistry" to cover the chemistries of every other element. That is more or less the state of things today. Biologists have encroached on biochemistry with molecular biology, bringing along their cellular frame of reference.

We credit Friedrich Wöhler, a 19th century German chemist, with undoing the notion of vitalism in chemistry. He synthesized urea, which had only ever been isolated from urine. The whole story is beautifully retold here. As part of an Internet wager, I tracked down the original letter from Wöhler to his erstwhile mentor, Professor Jakob Berzelius; I partially translated it from German:

Berlin, February 22, 1828

Dear Professor!

Although I surely hope that my letter of January 22nd and the post-script from February 2nd have arrived, I live every day, or rather every hour with the anxious hope to get a letter from you. I wanted to wait to write again but I cannot, so to say, "hold my chemical water" and must say that I can make urea without the use of kidneys or even an animal, whether it be human or canine. Ammonium cyanate is urea. [1]

Wöhler went on to describe how natural urea from urine, Pisse-Harnstoff, was the same as artificial urea.  He then ended with a possible "out" for the adherents to vitalism:

This artificial formation of urea--can it be an example of forming an organic substance from inorganic materials? It is remarkable that cyanic acid (and ammonia) are originally produced from an organic substance, and a natural philosopher would say that both come from an animal carbon, and from the resulting formed cyanic compounds, the organic has not yet disappeared, and therefore an organic body is produced yet again. 

Your Wöhler.

How Wöhler took the piss out of vitalism (so to speak) is a nice example of what T. H. Huxley meant when he later wrote:

The great tragedy of science, the slaying of a beautiful hypothesis by an ugly fact.

I got into a friendly wager over on Twitter after I discovered that both Wöhler and Huxley were credited with that pithy saying.

I tweeted: Who wrote "The great tragedy of science, the slaying of a beautiful hypothesis by an ugly fact."?

"T.H. Huxley" responded StarlessTwit

Not so fast I responded: "That's what the Internets would have you believe but there is this."  The link goes to a Wiki link crediting Wöhler with the saying.

I wagered that Wöhler had said it originally and that Huxley had been miscredited: link

That's when amba, the fact checker, weighed in, citing original source: "sorry to disappoint"

I can't finding anything close to what Huxley said in the original letters between Wöhler and Berzelius.  Wiki is wrong on this count.

Never bet against amba.

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[1] Wöhler treated cyanic acid, HOCN, with aqueous ammonia and generated ammonium cyanate, NH₄CNO. Ammonium cyanate is unstable and spontaneously rearranges to the more stable urea in situ:

Beryllium Is A Sweet Precious Gift

Different variations of beryl, including 1. golden beryl crystal, 2. heliodore. 3. emerald, 4. aquamarine, 5. morganite

The root word of beryllium is old and familiar and lurks beneath the surface of the commonly used word brilliant:

brilliant
1680s, from Fr. brilliant "sparkling, shining" prp. of briller "to shine" (16c.), from It. brillare "sparkle, whirl," perhaps from V.L. *berillare "to shine like a beryl," from berillus "beryl, precious stone," from L. beryllus (see beryl). In reference to diamonds (1680s) it means a flat-topped cut invented 17c. by Venetian cutter Vincenzo Peruzzi.

Beryl and emeralds were known to Pliny the Elder nearly 2000 years ago and he first observed a physical similarity between the two. In the Middle Ages, transparent, colorless beryl was used to make optical lenses, whence the German word Brille which today still means eyeglasses. The invention and manufacture of actual glass spectacles developed in Italy in the 13th century and improvements followed closely with the development of optics.

The minerologist R.-J. Haüy also observed the remarkable similarity between beryl and emerald (hardness and density), and he persuaded the pre-eminent chemist/pharmacist of his time (late 18th century) Louis Vauquelin (of Paris) to analyze the stones to see if they were chemically alike. In 1798, Vauquelin showed that both minerals contained not only alumina and silica as had previously been known, but also a new element, beryllium, which he extracted as the oxide from emerald. Fredrich Wöhler first prepared metallic beryllium by reducing BeCl_2, with potassium metal. Thus the new element beryllium was discovered.

One caveat: until around 1948, beryllium (symbol = Be) was also known as Glucinium (symbol Gl), reportedly because of the sweetish taste of its chloride salts.

WARNING: Beryllium is considered to be highly toxic so do not, repeat do not taste or chew your precious emeralds!